I was asked earlier to get in touch with somebody from DRN OC on behalf of GPC to try and figure out what cannot be extracted from the CDM and what kind of support can be provided to sites given the extra programming effort. I’m pushing to get distributed code. I’m still waiting on a response/phone call, so stay tuned for their response…
In the meantime, Marshfield does have some SAS code that we could potentially share, however there are few considerations: 1. We did not write code to extract the geographic location of patients and assumed 100% Midwest, as a very small percentage of our patients are located out of state. a. Would anybody have code that can be used to calculate these numbers for the other sites? 2. The LOINCs we included in our lab queries were pulled from our local i2b2 instance. Other sites would potentially use different LOINCs and would have to adjust the code accordingly 3. The code is not in the standard PMP format Let me know where a good place would be to post the code we have available. I’m not sure if it can be attached and distributed via email? [image006]Steffani Roush Research Programmer Analyst Senior | Office of Research Computing and Analytics Marshfield Clinic Research Institute Office: 715-221-6442 | Ext: 1-6442 From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> On Behalf Of Phillip Reeder Sent: Wednesday, August 28, 2019 12:03 PM To: Osinski, Kristen <kosin...@mcw.edu>; gpc-dev@listserv.kumc.edu Subject: [EXTERNAL] Re: PCORnet Descriptive Query & Supplemental Table [ACTION REQUIRED] Has anyone already written a query that can be shared? Or will each GPC site be writing their own version of the query. Phillip From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>> on behalf of "Osinski, Kristen" <kosin...@mcw.edu<mailto:kosin...@mcw.edu>> Date: Tuesday, August 27, 2019 at 1:15 PM To: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" <gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>> Subject: FW: PCORnet Descriptive Query & Supplemental Table [ACTION REQUIRED] See the below response from PCORnet DRN OC re: the Supplemental Table. It is indeed a separate manual request. Kristen Osinski, MS Business Analyst, Biomedical Informatics Clinical & Translational Science Institute Medical College of Wisconsin kosin...@mcw.edu<mailto:kosin...@mcw.edu> (414) 805-7245 (office) From: PCORnet DRN OC <dr...@pcornet.org<mailto:dr...@pcornet.org>> Date: Tuesday, August 27, 2019 at 12:15 PM To: "Osinski, Kristen" <kosin...@mcw.edu<mailto:kosin...@mcw.edu>> Subject: Re: PCORnet Descriptive Query & Supplemental Table [ACTION REQUIRED] ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hello Kristen, Thank you for your email. The information requested in the supplemental table are items that the PMP tools cannot currently query. We are hoping sites will be able to query their own EMR to provide the requested counts. We are working on developing PMP enhancements for future queries. I hope this was helpful and please do not hesitate to reach out with any further questions. Best, Kshema Nagavedu on behalf of the DRN OC QF Team On Tue, Aug 27, 2019 at 12:24 PM Osinski, Kristen <kosin...@mcw.edu<mailto:kosin...@mcw.edu>> wrote: Good morning, We have already returned the results for this Descriptives Query. Are you asking us to manually create and run queries to complete this additional form? Thanks! Kris Kristen Osinski, MS Business Analyst, Biomedical Informatics Clinical & Translational Science Institute Medical College of Wisconsin kosin...@mcw.edu<mailto:kosin...@mcw.edu> (414) 805-7245 (office) From: PCORnet DRN OC <dr...@pcornet.org<mailto:dr...@pcornet.org>> Date: Monday, August 26, 2019 at 3:53 PM To: PCORnet Query Fulfillment <q...@pcornet.org<mailto:q...@pcornet.org>>, "PCORnet 2.0 PIs" <pcornet2.0...@pcornet.org<mailto:pcornet2.0...@pcornet.org>>, "2.0 DataMart Administrators" <2.0datamartadministrat...@pcornet.org<mailto:2.0datamartadministrat...@pcornet.org>> Cc: "Darcy Louzao, Ph.D." <darcy.lou...@duke.edu<mailto:darcy.lou...@duke.edu>>, "Sturtevant,Jessica" <jessica_sturtev...@harvardpilgrim.org<mailto:jessica_sturtev...@harvardpilgrim.org>>, Keith Marsolo <keith.mars...@duke.edu<mailto:keith.mars...@duke.edu>>, Kshema <kshema_nagav...@harvardpilgrim.org<mailto:kshema_nagav...@harvardpilgrim.org>>, "Forrest, Christopher B" <forre...@email.chop.edu<mailto:forre...@email.chop.edu>>, Maryan Zirkle <mzir...@pcori.org<mailto:mzir...@pcori.org>> Subject: PCORnet Descriptive Query & Supplemental Table [ACTION REQUIRED] ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments. ________________________________ Hello PCORnet Colleagues, Two follow-up items related to the PCORI Descriptive Query (pcori_pmp_wp003): 1. Recently the DRN OC team asked DataMarts to hold on submitting the supplemental table, a part of the PCORI Descriptive Query (pcori_pmp_wp003), so that we could address questions received from multiple network partners. The v03 attached supplemental table for this descriptive query has been revised to reflect responses to these questions and clarifications regarding the type of output to be returned to the DRN OC. Please return the completed supplemental table to DRN OC (dr...@pcornet.org<mailto:dr...@pcornet.org>) by COB on September 9th, 2019. 2. As a number of DataMarts have noted that they are encountering very long program execution times, we ask that you contact DRN OC Query Fulfillment q...@pcornet.org<mailto:q...@pcornet.org> and we would be happy to help with troubleshooting and/or providing a modified query package to break up the size of the program. The DRN OC QF team will also work to break up packages of this size moving forward to avoid DataMarts encountering issues with execution times for distributed queries. Thank you for your help in completing the PCORI descriptive query supplemental table and for working with us to benchmark program/query size and execution time. If there are any questions, please reach out to QF at q...@pcornet.org<mailto:q...@pcornet.org>. Sincerely, Kshema Nagavedu on behalf of the DRN OC QF Team ________________________________ UT Southwestern Medical Center The future of medicine, today. ______________________________________________________________________ The contents of this message may contain private, protected and/or privileged information. If you received this message in error, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained within. Please contact the sender and advise of the erroneous delivery by return e-mail or telephone. Thank you for your cooperation.
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